A novel lineage of polyomaviruses identified in bark scorpions

Polyomaviruses are nonenveloped viruses with circular double stranded DNA genomes that range in size from ~4 to 7 kilobasepairs. Initially identified in mammals, polyomaviruses have now been identified in birds and a few fish species. Although fragmentary polyomavirus-like sequences have been detected as apparent 'hitchhikers' in shotgun genomics datasets for various arthropods, the possible diversity of these viruses in invertebrates remains unclear. In general, polyomaviruses are host-specific, showing strong evidence of host virus coevolution. Identification of polyomaviruses in a broader range of animals could shed useful light on the evolutionary history of this medically important group of viruses. Scorpions are predatory arachnids that are among the oldest terrestrial animals. Thus far, viromes of arachnids have been under sampled and understudied. Here, high throughput sequencing and traditional molecular techniques were used to explore the diversity of circular DNA viruses associated with bark scorpions (Centruroides sculpturatus) from the greater Phoenix area, Arizona, USA. The complete genomes of eight novel polyomaviruses were identified. Analysis of Centruroides transcriptomic datasets elucidated the splicing of the viral late gene array, which is more complex than that of vertebrate polyomaviruses. Phylogenetic analysis provides further evidence of co-divergence of polyomaviruses with their hosts, suggesting that at least one ancestral species of polyomaviruses was circulating amongst the primitive common ancestors of arthropods and chordates.

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Phylogeny of the Varidnaviria Morphogenesis Module: Congruence and Incongruence With the Tree of Life and Viral Taxonomy

Frontiers in Microbiology ◽

10.3389/fmicb.2021.704052 ◽

2021 ◽

Vol 12 ◽

Author(s):

Anthony C. Woo ◽

Morgan Gaia ◽

Julien Guglielmini ◽

Violette Da Cunha ◽

Patrick Forterre

Keyword(s):

Evolutionary History ◽

International Committee ◽

Tree Of Life ◽

Dna Viruses ◽

Origin And Evolution ◽

Double Stranded Dna ◽

Domains Of Life ◽

History Of ◽

Recent Classification ◽

Jelly Roll

Double-stranded DNA viruses of the realm Varidnaviria (formerly PRD1-adenovirus lineage) are characterized by homologous major capsid proteins (MCPs) containing one (kingdom: Helvetiavirae) or two β-barrel domains (kingdom: Bamfordvirae) known as the jelly roll folds. Most of them also share homologous packaging ATPases (pATPases). Remarkably, Varidnaviria infect hosts from the three domains of life, suggesting that these viruses could be very ancient and share a common ancestor. Here, we analyzed the evolutionary history of Varidnaviria based on single and concatenated phylogenies of their MCPs and pATPases. We excluded Adenoviridae from our analysis as their MCPs and pATPases are too divergent. Sphaerolipoviridae, the only family in the kingdom Helvetiavirae, exhibit a complex history: their MCPs are very divergent from those of other Varidnaviria, as expected, but their pATPases groups them with Bamfordvirae. In single and concatenated trees, Bamfordvirae infecting archaea were grouped with those infecting bacteria, in contradiction with the cellular tree of life, whereas those infecting eukaryotes were organized into three monophyletic groups: the Nucleocytoviricota phylum, formerly known as the Nucleo-Cytoplasmic Large DNA Viruses (NCLDVs), Lavidaviridae (virophages) and Polintoviruses. Although our analysis mostly supports the recent classification proposed by the International Committee on Taxonomy of Viruses (ICTV), it also raises questions, such as the validity of the Adenoviridae and Helvetiavirae ranking. Based on our phylogeny, we discuss current hypotheses on the origin and evolution of Varidnaviria and suggest new ones to reconcile the viral and cellular trees.

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Crustacean Genome Exploration Reveals the Evolutionary Origin of White Spot Syndrome Virus

Journal of Virology ◽

10.1128/jvi.01144-18 ◽

2018 ◽

Vol 93 (3) ◽

Cited By ~ 5

Author(s):

Satoshi Kawato ◽

Aiko Shitara ◽

Yuanyuan Wang ◽

Reiko Nozaki ◽

Hidehiro Kondo ◽

...

Keyword(s):

Evolutionary History ◽

White Spot Syndrome Virus ◽

Genomic Data ◽

White Spot ◽

Viral Pathogen ◽

Dna Viruses ◽

Double Stranded Dna ◽

History Of ◽

Phylogenetic Origin ◽

White Spot Syndrome

ABSTRACT White spot syndrome virus (WSSV) is a crustacean-infecting, double-stranded DNA virus and is the most serious viral pathogen in the global shrimp industry. WSSV is the sole recognized member of the family Nimaviridae, and the lack of genomic data on other nimaviruses has obscured the evolutionary history of WSSV. Here, we investigated the evolutionary history of WSSV by characterizing WSSV relatives hidden in host genomic data. We surveyed 14 host crustacean genomes and identified five novel nimaviral genomes. Comparative genomic analysis of Nimaviridae identified 28 “core genes” that are ubiquitously conserved in Nimaviridae; unexpected conservation of 13 uncharacterized proteins highlighted yet-unknown essential functions underlying the nimavirus replication cycle. The ancestral Nimaviridae gene set contained five baculoviral per os infectivity factor homologs and a sulfhydryl oxidase homolog, suggesting a shared phylogenetic origin of Nimaviridae and insect-associated double-stranded DNA viruses. Moreover, we show that novel gene acquisition and subsequent amplification reinforced the unique accessory gene repertoire of WSSV. Expansion of unique envelope protein and nonstructural virulence-associated genes may have been the key genomic event that made WSSV such a deadly pathogen. IMPORTANCE WSSV is the deadliest viral pathogen threatening global shrimp aquaculture. The evolutionary history of WSSV has remained a mystery, because few WSSV relatives, or nimaviruses, had been reported. Our aim was to trace the history of WSSV using the genomes of novel nimaviruses hidden in host genome data. We demonstrate that WSSV emerged from a diverse family of crustacean-infecting large DNA viruses. By comparing the genomes of WSSV and its relatives, we show that WSSV possesses an expanded set of unique host-virus interaction-related genes. This extensive gene gain may have been the key genomic event that made WSSV such a deadly pathogen. Moreover, conservation of insect-infecting virus protein homologs suggests a common phylogenetic origin of crustacean-infecting Nimaviridae and other insect-infecting DNA viruses. Our work redefines the previously poorly characterized crustacean virus family and reveals the ancient genomic events that preordained the emergence of a devastating shrimp pathogen.

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Evolution of the PRD1-adenovirus lineage: a viral tree of life incongruent with the cellular universal tree of life

10.1101/741942 ◽

2019 ◽

Author(s):

Anthony C. Woo ◽

Morgan Gaia ◽

Julien Guglielmini ◽

Violette Da Cunha ◽

Patrick Forterre

Keyword(s):

Evolutionary History ◽

Common Ancestor ◽

Tree Of Life ◽

Capsid Proteins ◽

Dna Viruses ◽

Universal Tree ◽

Double Stranded Dna ◽

Domains Of Life ◽

History Of ◽

Jelly Roll

AbstractDouble-stranded DNA viruses of the PRD1-adenovirus lineage are characterized by homologous major capsid proteins containing one or two β-barrel domains known as the jelly roll folds. Most of them also share homologous packaging ATPases of the FtsK/HerA superfamily P-loop ATPases. Remarkably, members of this lineage infect hosts from the three domains of life, suggesting that viruses from this lineage could be very ancient and share a common ancestor. Here we analyzed the evolutionary history of these cosmopolitan viruses by inferring phylogenies based on single or concatenated genes. These viruses can be divided into two supergroups infecting either eukaryotes or prokaryotes. The latter can be further divided into two groups of bacterioviruses and one group of archaeoviruses. This viral tree is thus incongruent with the cellular tree of life in which Archaea are closer to Eukarya and more divergent from Bacteria. We discuss various evolutionary scenarios that could explain this paradox.

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Phylogenomic Reconstruction Sheds Light on New Relationships and Timescale of Rails (Aves: Rallidae) Evolution

Diversity ◽

10.3390/d12020070 ◽

2020 ◽

Vol 12 (2) ◽

pp. 70 ◽

Cited By ~ 5

Author(s):

Juan C. Garcia-R ◽

Emily Moriarty Lemmon ◽

Alan R. Lemmon ◽

Nigel French

Keyword(s):

Evolutionary History ◽

State Of The Art ◽

Molecular Techniques ◽

Evolutionary Significance ◽

Phylogenetic Structure ◽

Bayesian Approaches ◽

Phylogenetic Studies ◽

Anchored Phylogenomics ◽

History Of ◽

Phylogenomic Analyses

The integration of state-of-the-art molecular techniques and analyses, together with a broad taxonomic sampling, can provide new insights into bird interrelationships and divergence. Despite their evolutionary significance, the relationships among several rail lineages remain unresolved as does the general timescale of rail evolution. Here, we disentangle the deep phylogenetic structure of rails using anchored phylogenomics. We analysed a set of 393 loci from 63 species, representing approximately 40% of the extant familial diversity. Our phylogenomic analyses reconstruct the phylogeny of rails and robustly infer several previously contentious relationships. Concatenated maximum likelihood and coalescent species-tree approaches recover identical topologies with strong node support. The results are concordant with previous phylogenetic studies using small DNA datasets, but they also supply an additional resolution. Our dating analysis provides contrasting divergence times using fossils and Bayesian and non-Bayesian approaches. Our study refines the evolutionary history of rails, offering a foundation for future evolutionary studies of birds.

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The past, present and future of ancient bacterial DNA

Microbial Genomics ◽

10.1099/mgen.0.000384 ◽

2020 ◽

Vol 6 (7) ◽

Cited By ~ 1

Author(s):

Nicolas Arning ◽

Daniel J. Wilson

Keyword(s):

Demographic Transition ◽

Dental Plaque ◽

Evolutionary History ◽

High Throughput Sequencing ◽

Industrial Revolution ◽

Environmental Isolates ◽

Bacterial Dna ◽

Content Type ◽

The Past ◽

History Of

Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis . Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.

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Genome Analysis of a Glossina pallidipes Salivary Gland Hypertrophy Virus Reveals a Novel, Large, Double-Stranded Circular DNA Virus

Journal of Virology ◽

10.1128/jvi.02588-07 ◽

2008 ◽

Vol 82 (9) ◽

pp. 4595-4611 ◽

Cited By ~ 59

Author(s):

Adly M. M. Abd-Alla ◽

François Cousserans ◽

Andrew G. Parker ◽

Johannes A. Jehle ◽

Nicolas J. Parker ◽

...

Keyword(s):

Salivary Gland ◽

Glossina Pallidipes ◽

Open Reading Frames ◽

Tsetse Flies ◽

Sequence Comparisons ◽

Dna Viruses ◽

Circular Dna ◽

Double Stranded Dna ◽

Salivary Gland Hypertrophy ◽

Salivary Gland Hypertrophy Virus

ABSTRACT Several species of tsetse flies can be infected by the Glossina pallidipes salivary gland hypertrophy virus (GpSGHV). Infection causes salivary gland hypertrophy and also significantly reduces the fecundity of the infected flies. To better understand the molecular basis underlying the pathogenesis of this unusual virus, we sequenced and analyzed its genome. The GpSGHV genome is a double-stranded circular DNA molecule of 190,032 bp containing 160 nonoverlapping open reading frames (ORFs), which are distributed equally on both strands with a gene density of one per 1.2 kb. It has a high A+T content of 72%. About 3% of the GpSGHV genome is composed of 15 sequence repeats, distributed throughout the genome. Although sharing the same morphological features (enveloped rod-shaped nucleocapsid) as baculoviruses, nudiviruses, and nimaviruses, analysis of its genome revealed that GpSGHV differs significantly from these viruses at the level of its genes. Sequence comparisons indicated that only 23% of GpSGHV genes displayed moderate homologies to genes from other invertebrate viruses, principally baculoviruses and entomopoxviruses. Most strikingly, the GpSGHV genome encodes homologues to the four baculoviral per os infectivity factors (p74 [pif-0], pif-1, pif-2, and pif-3). The DNA polymerase encoded by GpSGHV is of type B and appears to be phylogenetically distant from all DNA polymerases encoded by large double-stranded DNA viruses. The majority of the remaining ORFs could not be assigned by sequence comparison. Furthermore, no homologues to DNA-dependent RNA polymerase subunits were detected. Taken together, these data indicate that GpSGHV is the prototype member of a novel group of insect viruses.

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Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes

10.1101/2020.11.02.364562 ◽

2020 ◽

Author(s):

Spyros Lytras ◽

Gloria Arriagada ◽

Robert J. Gifford

Keyword(s):

Dna Sequences ◽

Evolutionary History ◽

Dna Viruses ◽

History Of ◽

Selective Forces ◽

Cenozoic Era ◽

Vertebrate Hosts ◽

New Perspective ◽

Animal Genomes

ABSTRACTHepadnaviruses (family Hepadnaviviridae) are reverse-transcribing animal viruses that infect vertebrates. Vertebrate genomes contain DNA sequences derived from ancient hepadnaviruses, and these ‘endogenous hepatitis B viruses’ (eHBVs) reveal aspects of the long-term coevolutionary relationship between hepadnaviruses and their vertebrate hosts. Here, we use a novel, data-oriented approach to recover and analyse the complete repertoire of eHBV elements in published animal genomes. We show that germline incorporation of hepadnaviruses is exclusive to a single vertebrate group (Sauria) and that the eHBVs contained in saurian genomes represent a far greater diversity of hepadnaviruses than previously recognised. Through in-depth characterisation of eHBV elements we establish the existence of four distinct subgroups within the genus Avihepadnavirus and trace their evolution through the Cenozoic Era. Furthermore, we provide a completely new perspective on hepadnavirus evolution by showing that the metahepadnaviruses (genus Metahepadnavirus) originated >300 million years ago in the Paleozoic Era, and has historically infected a broad range of vertebrates. We also show that eHBVs have been intra-genomically amplified in some saurian lineages, and that eHBVs located at approximately equivalent genomic loci have been acquired in entirely distinct germline integration events. These findings indicate that selective forces have favoured the accumulation of hepadnaviral sequences at specific loci in the saurian germline. Our investigation provides a range of new insights into the long-term evolutionary history of reverse-transcribing DNA viruses and demonstrates that germline incorporation of hepadnaviruses has played an important role in shaping the evolution of saurian genomes.

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Impacts of Genome-Wide Analyses on Our Understanding of Human Herpesvirus Diversity and Evolution

Journal of Virology ◽

10.1128/jvi.00908-17 ◽

2017 ◽

Vol 92 (1) ◽

Cited By ~ 19

Author(s):

Daniel W. Renner ◽

Moriah L. Szpara

Keyword(s):

High Throughput Sequencing ◽

Evolutionary Dynamics ◽

Human Herpesvirus ◽

Ribosome Profiling ◽

Genomic Diversity ◽

Rna Seq ◽

Dna Viruses ◽

Double Stranded Dna ◽

Genome Wide ◽

Human Herpesviruses

ABSTRACTUntil fairly recently, genome-wide evolutionary dynamics and within-host diversity were more commonly examined in the context of small viruses than in the context of large double-stranded DNA viruses such as herpesviruses. The high mutation rates and more compact genomes of RNA viruses have inspired the investigation of population dynamics for these species, and recent data now suggest that herpesviruses might also be considered candidates for population modeling. High-throughput sequencing (HTS) and bioinformatics have expanded our understanding of herpesviruses through genome-wide comparisons of sequence diversity, recombination, allele frequency, and selective pressures. Here we discuss recent data on the mechanisms that generate herpesvirus genomic diversity and underlie the evolution of these virus families. We focus on human herpesviruses, with key insights drawn from veterinary herpesviruses and other large DNA virus families. We consider the impacts of cell culture on herpesvirus genomes and how to accurately describe the viral populations under study. The need for a strong foundation of high-quality genomes is also discussed, since it underlies all secondary genomic analyses such as RNA sequencing (RNA-Seq), chromatin immunoprecipitation, and ribosome profiling. Areas where we foresee future progress, such as the linking of viral genetic differences to phenotypic or clinical outcomes, are highlighted as well.

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Evolutionary history of bacteriophages with double-stranded DNA genomes

Biology Direct ◽

10.1186/1745-6150-2-36 ◽

2007 ◽

Vol 2 (1) ◽

pp. 36 ◽

Cited By ~ 25

Author(s):

Galina Glazko ◽

Vladimir Makarenkov ◽

Jing Liu ◽

Arcady Mushegian

Keyword(s):

Evolutionary History ◽

Double Stranded Dna ◽

History Of

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Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes

10.1101/455816 ◽

2018 ◽

Cited By ~ 3

Author(s):

Julien Guglielmini ◽

Anthony Woo ◽

Mart Krupovic ◽

Patrick Forterre ◽

Morgan Gaia

Keyword(s):

Phylogenetic Trees ◽

Dna Viruses ◽

Double Stranded Dna ◽

Virion Morphogenesis ◽

History Of ◽

Eukaryotic Dna ◽

Dsdna Viruses ◽

Virion Formation

AbstractGiant and large eukaryotic double-stranded DNA viruses from the Nucleo-Cytoplasmic Large DNA Virus (NCLDV) assemblage represent a remarkably diverse and potentially ancient component of the eukaryotic virome. However, their origin(s), evolution and potential roles in the emergence of modern eukaryotes remain a subject of intense debate. Since the characterization of the mimivirus in 2003, many big and giant viruses have been discovered at a steady pace, offering a vast material for evolutionary investigations. In parallel, phylogenetic tools are constantly being improved, offering more rigorous approaches for reconstruction of deep evolutionary history of viruses and their hosts. Here we present robust phylogenetic trees of NCLDVs, based on the 8 most conserved proteins responsible for virion morphogenesis and informational processes. Our results uncover the evolutionary relationships between different NCLDV families and support the existence of two superclades of NCLDVs, each encompassing several families. We present evidence strongly suggesting that the NCLDV core genes, which are involved in both informational processes and virion formation, were acquired vertically from a common ancestor. Among them, the largest subunits of the DNA-dependent RNA polymerase were seemingly transferred from two clades of NCLDVs to proto-eukaryotes, giving rise to two of the three eukaryotic DNA-dependent RNA polymerases. Our results strongly suggest that these transfers and the diversification of NCLDVs predated the emergence of modern eukaryotes, emphasizing the major role of viruses in the evolution of cellular domains.

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